title: RRBS-analyser: a comprehensive web server for reduced representation bisulfite sequencing data analysis.
abstract: In reduced representation bisulfite sequencing (RRBS), genomic DNA is digested with the restriction enzyme and then subjected to next-generation sequencing, which enables detection and quantification of DNA methylation at whole-genome scale with low cost. However, the data processing, interpretation, and analysis of the huge amounts of data generated pose a bioinformatics challenge. We developed RRBS-Analyser, a comprehensive genome-scale DNA methylation analysis server based on RRBS data. RRBS-Analyser can assess sequencing quality, generate detailed statistical information, align the bisulfite-treated short reads to reference genome, identify and annotate the methylcytosines (5mCs) and associate them with different genomic features in CG, CHG, and CHH content. RRBS-Analyser supports detection, annotation, and visualization of differentially methylated regions (DMRs) for multiple samples from nine reference organisms. Moreover, RRBS-Analyser provides researchers with detailed annotation of DMR-containing genes, which will greatly aid subsequent studies. The input of RRBS-Analyser can be raw FASTQ reads, generic SAM format, or self-defined format containing individual 5mC sites. RRBS-Analyser can be widely used by researchers wanting to unravel the complexities of DNA methylome in the epigenetic community. RRBS-Analyser is freely available at http://122.228.158.106/RRBSAnalyser/.
authors.affiliation: Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325035, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Wang
authors.forename: Qi
authors.initials: Q
authors.lastname: Liu
authors.forename: Xianfeng
authors.initials: X
authors.lastname: Li
authors.forename: Xiaobing
authors.initials: X
authors.lastname: Wang
authors.forename: Jinchen
authors.initials: J
authors.lastname: Li
authors.forename: Xiaochun
authors.initials: X
authors.lastname: Zhu
authors.forename: Zhong Sheng
authors.initials: ZS
authors.lastname: Sun
authors.forename: Jinyu
authors.initials: J
authors.lastname: Wu
mesh_terms: D019295:Computational Biology / Q000379:methods*; D019175:DNA Methylation; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D017422:Sequence Analysis, DNA; D064878:Web Browser; D057188:Workflow
keywords: RRBS; differentially methylated region; epigenetics; methylation; next-generation sequencing